EP4105228A1 - Polypeptide antigénique du sras-cov-2, virus adéno-associé recombinant de celui-ci, et utilisation dans la préparation de vaccin - Google Patents

Polypeptide antigénique du sras-cov-2, virus adéno-associé recombinant de celui-ci, et utilisation dans la préparation de vaccin Download PDF

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EP4105228A1
EP4105228A1 EP20891416.8A EP20891416A EP4105228A1 EP 4105228 A1 EP4105228 A1 EP 4105228A1 EP 20891416 A EP20891416 A EP 20891416A EP 4105228 A1 EP4105228 A1 EP 4105228A1
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associated virus
antigen polypeptide
recombinant adeno
sequence
sars
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EP4105228A4 (fr
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Zexin Zhou
Zhongqiu Liu
Guochao Liao
Huapeng Li
Chao Zhang
Xiaoxiao Qi
Junlin Chen
Deying YANG
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Hengda Biomedical Technology Co Ltd
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Hengda Biomedical Technology Co Ltd
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Definitions

  • the present disclosure relates to the field of biotechnology, in particular, to a SARS-COV-2 antigen polypeptide, its recombinant adeno-associated virus, and its use in preparing a vaccine.
  • Coronaviruses belong to a large class of RNA viruses that exists widely in nature and can only infect vertebrates. In humans, coronaviruses can cause severe respiratory illnesses such as colds, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS).
  • SARS severe acute respiratory syndrome
  • MERS Middle East respiratory syndrome
  • SARS-COV-2 Since the end of 2019, a new type of coronavirus, SARS-COV-2, has caused a global pandemic of novel coronavirus pneumonia (COVID-19). SARS-COV-2 is highly latent and contagious. It causes not only asymptomatic infection, but also viral pneumonia, severe respiratory syndrome, renal failure, and death. Therefore, the development of a vaccine against COVID-19 is extremely important and urgent.
  • the SARS-COV-2 spike glycoprotein invades the body by binding to the angiotensin-converting enzyme 2 (ACE2) receptor on a cell human in the human body, hence the spike glycoprotein is a key target for vaccine development.
  • ACE2 angiotensin-converting enzyme 2
  • Wild-type adeno-associated virus is a DNA virus with a diameter of about 22 nm and is not pathogenic to humans.
  • the recombinant AAV obtained by genetic engineering of wild-type AAV has become a safe and effective delivery vector in gene therapy.
  • AAV vectors are widely used in the development of vaccines, tumor drugs, and genetic disease drugs.
  • the advantages of using AAV vectors to deliver antigen genes are that AAV vectors have very low auto-immunogenicity and genotoxicity; they could be highly efficiently delivered and they maintain long-term expression.
  • AAV vector vaccines can be used to induce the production of antibodies by an endogenous antigen, and the production of antibodies is continuous and stable.
  • the primary objective of the present disclosure is to provide a novel coronavirus (SARS-COV-2) antigen polypeptide.
  • Another objective of the present disclosure is to provide a recombinant adeno-associated virus expressing the antigen polypeptide.
  • Yet another objective of the present disclosure is to provide a use of the recombinant adeno-associated virus above in preparing a COVID-19 vaccine.
  • a novel coronavirus (SARS-COV-2) antigen polypeptide wherein an amino acid sequence of the antigen polypeptide is one of the following:
  • SEQ ID NO.1 the sequence of amino acids 331 - 583 encoded by the gene sequence of SARS-COV-2 (GenBank accession no. NC_045512.2) is predicted to be a spike protein receptor domain, which is a target for inducing antibody production and preparing vaccine;
  • SEQ ID NO.2 the sequence of amino acids 319 - 541 encoded by the gene sequence of SARS-COV-2 (GenBank accession no. NC_045512.2) is predicted to be a spike protein receptor domain, which is a target for inducing antibody production and preparing vaccine;
  • An expression vector of the aforementioned antigen peptide comprising an adeno-associated virus inverted terminal repeat sequence (ITR sequence), a nucleotide sequence encoding a signal peptide, and a nucleotide sequence encoding the antigen peptide.
  • ITR sequence adeno-associated virus inverted terminal repeat sequence
  • the expression vector also comprises an essential expression regulatory element, such as a promoter sequence, an upstream regulatory region, a coding region, a transcription regulatory element, a terminator, among others.
  • an essential expression regulatory element such as a promoter sequence, an upstream regulatory region, a coding region, a transcription regulatory element, a terminator, among others.
  • the nucleotide sequence encoding the signal peptide is optimized by human codons.
  • the inverted terminal repeat sequence is from serotype AAV2.
  • the signal peptide is preferably an IgE signal peptide.
  • a recombinant adeno-associated virus expressing the antigen polypeptide, its preparation method comprises co-incubating pHelper, pRep2Cap5, and the expression vector, transfecting a cell in the presence of polyethyleneimine as a transfection reagent; culturing the cell, then collecting the cell by centrifugation, performing lysis and purification to obtain a purified liquid comprising the recombinant adeno-associated virus.
  • the pRep2Cap5 corresponds to serotype AAV5.
  • rAAV vectors can be produced by methods known to those skilled in the art. Those skilled in the art can use a well-known method based on HEK293 three-plasmid system to produce rAAV vectors, for example, as disclosed in Chinese invention patent ZL201710553164.0.
  • Those skilled in the art can also construct expression plasmids and serotype plasmids based on an insect system of an SF9 cell line to produce rAAVs, for example, as disclosed in Chinese patent publication CN108699567A .
  • expression plasmids and serotype plasmids based on an insect system of an SF9 cell line to produce rAAVs, for example, as disclosed in Chinese patent publication CN108699567A .
  • herpes-virus-based or adenovirus-based packaging systems etc.
  • rAAVs After rAAVs are produced, they can be purified from host cells by a variety of conventional purification methods such as physical lysis, chemical lysis, filtration and clarification, tangential flow ultrafiltration, column chromatography, CsCl gradient centrifugation, and iodixanol centrifugation.
  • purification methods such as physical lysis, chemical lysis, filtration and clarification, tangential flow ultrafiltration, column chromatography, CsCl gradient centrifugation, and iodixanol centrifugation.
  • the recombinant adeno-associated virus above can be used to prepare a vaccine for COVID-19.
  • the vaccine comprises a pharmaceutically acceptable diluent and/or a pharmaceutically acceptable excipient.
  • the vaccine can be prepared as injections for intranasal and intramuscular injection.
  • the present invention has the following advantages and effects:
  • SARS-COV-2 antigen polypeptide sequence predicted in the present disclosure has the following advantages as illustrated by experiments: a. compared with an intact S protein or the S1 subunit as an antigen, a truncated domain sequence has higher specificity as a result of a shorter sequence, a smaller molecular weight, and a more defined structure; b.
  • a serum antibody neutralization test showed that the antigen polypeptide of the present disclosure has high immunogenicity and can produce powerful protective neutralizing antibodies; c. for the first time, it is reported that the SARS-COV-2 antigen polypeptide nucleic acid sequence is delivered in the AAV5 recombinant adeno-associated virus by intramuscular injection, and the antigen sequence is expressed effectively and continuously.
  • the rAAV composition of the present disclosure is delivered and expressed in vivo to produce a fusion antigen polypeptide, induces the production of serum neutralizing antibodies, which have a neutralizing titer to the novel SARS-COV-2 coronavirus and are expressed continuously; the rAAV composition can be used to immunize humans against the novel coronavirus pneumonia COVID-19.
  • S protein also known as spike protein, is a capsid surface glycoprotein of a coronavirus.
  • Novel coronavirus SARS-COV-2 binds to the human ACE2 receptor through the S protein and invades cells.
  • a truncated S protein as an antigen is obtained by predicting and intercepting part region of the S protein.
  • a vector is a delivery vehicle or element for a genetic material.
  • examples of a vector include a plasmid, a virus, a virus-like particle, and a bacteriophage.
  • the vector is often referred to as “cloning vector”, “expression vector” or “backbone vector”, and “viral vector” in different applications or scenarios.
  • rAAV vector refers to a recombinant non-replicating adeno-associated virus.
  • the rAAV vector includes a serotype protein capsid and encapsulates a recombinant genome.
  • the genome includes functional 5' and 3' inverted terminal repeats sequences (ITR sequences).
  • ITR sequences are flanked by exogenous nucleotide sequences that replaced rep or cap genes found in wild-type AAVs. ITR sequences provide functional rescue, replication, and packaging to rAAVs.
  • the ITR sequences are from AAV2.
  • Exogenous nucleotide sequences usually consist of a series of expression regulatory elements and coding regions.
  • An AAV serotype plasmid pREPCAP includes two open reading frames (ORFs) that encode the expression products of Rep and Cap.
  • Cap refers to a capsid protein of AAV familiar to those skilled in the art.
  • Cap encodes functional proteins such as capsid proteins VP1, VP2, VP3, and AAP.
  • AAVs of different serotypes have different capsid protein sequences.
  • An AAV helper plasmid pHelper usually contains coding regions such as adeno-associated virus VA RNA, E4 ORF6, E2A, and E1B, which provide functions necessary for AAV replication.
  • Expression regulatory elements are generally a collection of promoter sequences, upstream regulatory regions, coding regions, and transcriptional regulatory elements, which jointly realize replication, transcription and translation of coding region sequences in receptor cells.
  • a promoter is a DNA sequence that is recognized and bound by RNA polymerase, and initiates transcription.
  • the promoter contains conserved sequences required for RNA polymerase specific binding and transcription initiation, most of which are located upstream of the transcription initiation point of structural genes; the promoter itself is not transcribed.
  • a CAG promoter is selected as the promoter sequence.
  • Suitable promoters also include promoters known to those skilled in the art, such as human cytomegalovirus (CMV) promoter, ubiquitin C promoter (UbC), and EF1 ⁇ promoter.
  • CMV human cytomegalovirus
  • UbC ubiquitin C promoter
  • promoters can be selected to regulate the expression of mRNA transcription.
  • SV40 polyA is selected as a transcriptional terminator.
  • Suitable polyA sequences include but are not limited to SV40 polyA, BGH polyA, synthetic polyA, etc. known in the art.
  • Some examples also include transcription-enhancing regulatory elements, such as woodchuck hepatitis virus post-transcriptional regulatory elements (WPREs) and sequences that increase translation efficiency (Kozak sequences).
  • WPREs woodchuck hepatitis virus post-transcriptional regulatory elements
  • SARS-COV-2 GenBank accession no. NC_045512.2
  • NCBI database https://www.ncbi.nlm.nih.gov/genbank.
  • conserved domains within the gene sequence were predicted by NCBI Conserved Domain Search (https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi).
  • the prediction result showed that the spike receptor-binding domain was the sequence of amino acids 331 - 583 (SEQ ID NO.1). Based on our own technical knowledge, the C-terminal sequence of the domain was extended by 10 amino acids (ILDITPCSFG, SEQ ID NO. 3). This was to enrich the cysteine from the original sequence in the C-terminal to facilitate antigen aggregation.
  • the sequence obtained was spliced after the IgE signal peptide; human codon optimization was performed by GenSmart Optimization (Version Beta 1.0).
  • the primers were designed by DNAWorks (v3.2.4) (https://hpcwebapps.cit.nih.gov/dnaworks/); the synthesized sequence was amplified by PrimeSTAR ® HS DNA Polymerase (Takarabio). Endonucleases FastDigest TM EcoRI and FastDigest TM HindIII (ThermoFisher) were used to digest the adeno-associated virus backbone vector pAAV-CAG-MCS-WPRE-SV40polyA.
  • ClonExpress MultiS One Step Cloning Kit recombination kit (VAZYME, Nanjing) was used for homologous recombination ligation reactions. Products of the ligation reaction were transformed into Escherichia coli DH5 ⁇ and spread on an ampicillin-resistant petri dish. 16 hours later, bacterial colonies were selected for further examination. The positive clones were sent to a sequencing company (GENEWIZ, Suzhou) for sequencing (SEQ ID NO.4). The plasmid with the correct sequencing result was named pAAV-NS001 vector, and its components are shown in FIG. 1 .
  • SARS-COV-2 GenBank accession no. NC_045512.2
  • NCBI database https://www.ncbi.nlm.nih.gov/genbank.
  • conserved domains within the sequence were predicted by Uniprot blast (https://www.uniprot.org/blast/) through uniprotkb_refprotswissprot database.
  • the prediction result showed that the spike receptor-binding domain was the sequence of amino acids 319 - 541.
  • the sequence obtained and an IgE signal peptide were spliced into a new gene sequence; human codon optimization was performed by GenSmart Optimization (Version Beta 1.0).
  • the primers were designed by DNAWorks (v3.2.4) (https://hpcwebapps.cit.nih.gov/dnaworks/); the synthesized codon-optimized sequence was amplified by PrimeSTAR ® HS DNA Polymerase (Takarabio). Endonucleases FastDigest TM EcoRI and FastDigest TM HindIII (ThermoFisher) were used to digest the adeno-associated virus backbone vector pAAV-CAG-MCS-WPRE-SV40polyA. ClonExpress MultiS One Step Cloning Kit recombination kit (VAZYME, Nanjing) was used for homologous recombination ligation reactions.
  • 293T cells were inoculated in a 150 mm petri dish at a density of 1 ⁇ 10 7 cells per petri dish 24 hours before transfection, and 12 ⁇ g pHelper, 8 ⁇ g pRep2Cap5, 5 ⁇ g pAAV-NS001 (or 5 ⁇ g pAAV-NS002) and 10 ⁇ g polyethyleneimine (25 kD) as a transfection reagent were added to incubate transfection. 72 hours after the transfection, the cells were harvested by centrifugation at 500 ⁇ g for 5 min at 4°C. The cells were resuspended in a lysis buffer containing 50 mM Tris-HCl (pH 8.0) and 150 mM NaCl.
  • the harvested lysate was subjected to three freeze-thaw cycles in dry ice/ethanol and 37°C water bath successively, then 1 unit/mL of nuclease and 0.5% sodium deoxycholate were added, the resulting cell suspension was incubated at 37°C for 1 hour.
  • the cell suspension was centrifuged at 5000 ⁇ g for 20 minutes, rAAV supernatant crude lysate was collected at 4°C.
  • the crude lysate was diluted with 10 mM Tris-HCl (pH 8.0) buffer to a final volume of 10 ml, then iodixanol was added into a 39 ml ultracentrifuge tube according to a mass-to-volume ratio gradient of 15%, 25%, 40%, and 60%.
  • the mixture obtained was centrifuged at 350,000 ⁇ g for 1 hour at 18 °C, 3 ml of 40% lower fraction and 0.5 ml of 60% upper fraction were collected as a purified solution.
  • the purified solution was replaced with a virus preservation solution by ultrafiltration with a 100 kDa cut-off ultrafiltration tube (Millipore).
  • the recombinant virus preservation solution was a PBS phosphate buffer (pH 7.4) , 0.05% Poloxamer 188.
  • the purified rAAVs were labeled NS001, NS002, and viral titers were determined by SYBRGreenI qPCR. NS001 and NS002 were stored in a refrigerator at -80°C before use.
  • mice aged 5-6 weeks were randomly selected for intramuscular injection of NS001 (titer of 1 ⁇ 10 12 GC/mL, injection volume of 200 ⁇ L). Serums of pre-immunization mice were taken as the negative control.
  • Five BALB/c mice aged 5-6 weeks were randomly selected and immunized with recombinant green fluorescent protein adeno-associated virus vector; serums of the 5 immunized mice were used as a vector blank control.
  • a program of an initial immunization and a second booster immunization was adopted. Injections were carried out on day 0 and day 30. Blood was taken on day 30 and day 40; 0.1- 0.2 mL of blood was taken from each mouse and was placed at 0°C for 60 minutes. Centrifugation was performed at 4000 rpm for 15 minutes; the upper serum was taken for ELISA analysis and antibody neutralization experiments.
  • ELISA was used to detect the immune effect of mouse serum on day 30: Recombinant spike protein RBD-His was dissolved in 0.1 M carbonate buffer (pH 9.6) to prepare a solution at a concentration of 1 ⁇ g/mL. The solution was added into a 96-well plate (100 ⁇ L per well), and incubated overnight at 4°C. The next day, the solution was incubated at 37°C for one hour; then the plate was washed 3 times with PBST (PBS+ 0.1% Tween-20) (300 ⁇ L/well/time). After washing, 250 ⁇ L of 2% skimmed milk powder was added into each well, and was incubated at room temperature for 1 hour, before washed 3 times with PBST.
  • PBST PBS+ 0.1% Tween-20
  • Serum samples of 5 mice in the same group were each diluted 300 times with PBS; the diluted serum samples were added to a 96-well plate (100 ⁇ L per well), and three secondary wells were made in parallel for each dilution gradient. Incubation was carried out in a 37°C incubator for two hours, the plate was washed 3 times. HRP (horseradish peroxidase) labeled IgG secondary antibody and IgM secondary antibody were diluted 5000 times, before being added to each well (100 ⁇ L per well) and incubated at room temperature for 1 hour; the plate was washed 3 times. 100 ⁇ L TMB solution was added to each well, followed by color development in the dark at room temperature for 20 min.
  • HRP horseradish peroxidase
  • the IgM antibodies in the 300 ⁇ diluted serum had an average OD IgM of 1.494 ⁇ 0.024, while in the AAV-GFP control group, the average OD IgM was 0.211 ⁇ 0.020). This proved that high titers of IgM antibodies were produced in the mice; the mice were IgM positive. Generally, during viral infection, before generating an adaptive high-affinity IgG response, IgM antibodies provide the first line of defense and play an important role in short-term immunity.
  • the IgG antibodies in the 300 ⁇ diluted serum had an average OD IgG of 2.910 ⁇ 0.083, while in the AAV-GFP control group, the average OD IgG was 0.230 ⁇ 0.018). Thist proved that high titers of IgG antibodies were produced in the mice; the mice were IgG positive. This showed that the vaccine induced a strong immune response in the mice, and played an important role in long-term immunity and immune memory.
  • Pre-immune serums and AAV-GFP infected serums were used as controls, and NS001 serogroup was the test group.
  • Vero E6 cells were inoculated into a 96-well plate (2 ⁇ 10 4 cells/well) and cultured overnight with 5% CO 2 at 37°C. On the second day, the serum samples were inactivated by heating at 56°C for 30 min. Then, they were 4-fold serial diluted with a DMEM medium containing 2% FBS to produce a set of serially diluted serums to be tested.
  • 100 TCID50 of SARS-COV-2 (strain number: 2020XN4276, provided and tested by a biosafety level 3 laboratory in Guangdong Provincial Center for Disease Control and Prevention) was respectively mixed with a set of 4-fold serial diluted serums to be tested, and the mixture was incubated at 37°C for 1 h, followed by adding cultured Vero E6 cells.
  • wells containing cells infected by 100 TCID50 of SARS-COV-2 were positive quality control wells, while wells containing cells added with 0.1 TCID50 of the virus were negative control wells.
  • CPE cytopathic effect
  • the neutralization test showed that the ND50 titer of neutralizing antibodies was 1/128, indicating that NS001 formulation can produce neutralizing antibody activity against SARS-COV-2 and protect cells from SARS-COV-2 infection.
  • the results showed that the NS001 vaccine induced humoral immune response, had a strong neutralizing activity in humoral immune response and protected cells from SARS-COV-2 infection.
  • the grouping of experimental animals, the immunization protocol, the method of obtaining serums and the immune effect detection method were the same as those of Example 4.
  • mice serums of five immunized BALB/c mice aged 5-6 weeks were collected to determine the immune effect. Please refer to the detection method of Example 4, ELISA was used to determine the immune effect of mice serums on day 30.
  • the IgG antibodies in the 300 ⁇ diluted serum had an average OD IgG of 2.340 ⁇ 0.205
  • the IgM antibodies in the 300 ⁇ diluted serum had an average OD IgM of 1.794 ⁇ 0.045
  • the average OD IgG was 0.230 ⁇ 0.018
  • the average OD IgM was 0.211 ⁇ 0.020.
  • the mice were IgG and IgM positive. This showed that the vaccine induced a strong immune response in the mice.
  • the serum neutralization test was performed according to the method of Example 5, and the results are shown in FIG. 6 .
  • the neutralization test showed that the ND50 titer of neutralizing antibodies was 1/64.
  • the results showed that the NS002 vaccine induced humoral immune response, had a strong neutralizing activity in humoral immune response and protected cells from SARS-COV-2 infection.

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